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QSutils

Set of utility functions in viral quasispecies analysis with NGS data. Most are equally usefull in metagenomic studies. There are three main types of functions: (1) data manipulation and exploration; functions useful in converting reads to haplotypes and frequencies, repairing reads, intersecting strand haplotypes, and to visualize haplotype alignments. (2) diversity indices; functions to compute diversities and entropies; incidence, abundance and fuctional indices are considered. (3) data simulation; functions useful in generating random viral quasispecies data.

How to install the package

library(devtools)
install_git("https://github.com/VHIRHepatiques/QSutils")

library(QSutils)

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R package to compute quasispecies diversity (currently under development).

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